Polymer Chemistry Mixture
This article delves into the utilization of molecular dynamics simulations with tools such as pymatgen, lammps, and openFF. It discusses interatomic potentials and force field generation processes in organic chemistry. Additionally, it covers accessing density data from multiple sources.
interatomic potentials:
https://www.ctcms.nist.gov/potentials/
https://zhuanlan.zhihu.com/p/351829537
https://www.ctcms.nist.gov/potentials/system/C-H-O/
https://atb.uq.edu.au/index.py?tab=structure_search
https://github.com/dwsideriusNIST/LAMMPS_Examples
opensmog smog2.provides force field generation tool
run simulation under given temperature, pressure and get density
openmm
generate force field on the fly:
from openff.toolkit.topology import Molecule
molecule = Molecule.from_smiles(‘c1ccccc1’)
pymatgen contains polymer generator to lammps:
pymatgen.io.lammps.utils
simulating reaction in molecular dynamics:
implemented in lammps fix bond/react method
random.randomvoidmail@erine.email (pending approval)
seen polymer names on lammps demo website:
https://lammps.org/pictures.html#reactphoto
https://docs.lammps.org/Intro_features.html
If you are a new computational chemist I would advise you to use ASE, it is not only useful for nanoparticles, I’m using it nearly every day.
patent:
http://chemdataextractor.org/results/26088052-3833-41ea-98f1-0a8a3fb2c341
https://www.zhihu.com/question/50559712
moltemplate, packmol
vmd: lammps data file visualization
build input file for lammps:
get retrosynthesis training data on picture search engines
octa: predict polymer properties
https://octa.jp/references/examples/
Link: [5]http://oexchange.org/spec/0.8/rel/related-target
You can try [33]https://spaya.ai/ it is a retro-synthetic analysis
[37]Http://www.orgsyn.org/
[41]Http://www.orgsyn.org/
[45]Http://www.organic-chemistry.org/
Try this interesting blog: [49]http://totallysynthetic.com/blog/
And also this website: [50]http://chemistrybydesign.oia.arizona.edu/
[54]http://www.chemspider.com/
[58]https://pubchem.ncbi.nlm.nih.gov/search
Organic Syntheses Website: <[62]http://www.orgsyn.org
Organic Chemistry Portal: <[63]http://www.organic-chemistry.org/abstracts
Chemsynthesis: [64]http://www.chemsynthesis.com
ChemExper: [65]https://www.chemexper.com
Pub Chem compound: [67]http://pubchem.ncbi.nlm.nih.gov
E-molecules: [68]http://www.emolecules.com
Chemspider: [69]http://www.chemspider.com
Reaxys: [70]https://www.reaxys.com/
SciFinder: [71]http://www.cas.org,
STN: [72]https://stnweb.cas.org/
[80]https://www.vulcanchem.com/
gromacs: creating polymer structure
http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Polymers
latest gromacs documentation:
https://manual.gromacs.org/documentation/
online organic chemistry textbook:
https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/intro1.htm
openbabel can only run normally on x86 platforms. so do other cheminfo packages.
sources of organic synthesis
https://www.organic-chemistry.org
What is matsci.org?
matsci.org is a community forum for the discussion of anything materials science, with a focus on computational materials science research. Its members are typically from academic research institutions and universities.
People that currently help run matsci.org include maintainers of the following codes and collaborations:
OVITO
GULP
DL_POLY
OPTIMADE
pyiron
hiphive
ASE
MPDS
iFermi
LAMMPS
MaRDA
exciting
JARVIS
and members of the following research groups:
Hacking Materials Group
Persson Group
Materials Virtual Lab
Materials Intelligence
translate bigsmiles into smiles
polymer database:
PolyInfo and NIST Synthetic Polymer MALDI Recipes database
USPEX
chemdraw chemoffice indraw spaya.ai
reaxys scifinder-n
marvin sketch pka
https://github.com/PKUMDL-AI/AutoSynRoute
polymer simulation:
material studio
amsterdam modeling suite
cp2k orca
https://orcaforum.kofo.mpg.de/app.php/portal
chemistry in stack exchange:
https://chemistry.stackexchange.com/
polymer retrosynthesis using retro*:
seq2seq-retro mlp-retro polyretro-uspto
deepchem, chempy(inorganic)
avogadro: import openbabel files
odachi: decompose target molecular into source molecular, highlight the potential bond
rdkit: python chemistry informatic
polymer informatic
ab initio chemistry:
lammps, quantum espresso, nwchem, gamess, uspex
from https://www.webmol.net:
Gamess, Gaussian, MolPro, Mopac, NWChem, Orca, PQS, PSI, Q-Chem, TeraChem, Tinker, Quantum Expresso, and VASP